NAD+-Dependent Cohesin Decline Drives Sex‑Dimorphic TAD Insulation Loss and Ectopic Neuronal Programming in Aged MuSCs

Hypothesis

Age-associated decline in NAD+ levels reduces cohesin complex loading onto chromatin, leading to progressive loss of TAD insulation. This architectural collapse permits ectopic enhancer-promoter contacts that activate neuronal gene programs and inflammatory pathways in aged muscle stem cells (MuSCs). The effect is more pronounced in males because estrogen-dependent up-regulation of the NAD+ salvage pathway preserves NAD+ and cohesin activity in females[1][2].

Mechanistic Model

• NAD+ shortage → diminished activity of NAD+-dependent enzymes (e.g., SIRT1, PARP1) that facilitate cohesin acetylation and stabilization[3].
• Cohesin hypo‑loading → weakened loop extrusion, causing TAD boundary erosion (≈38% loss in geriatric vs 20% in old MuSCs)[1].
• Boundary loss → enhancers normally restricted to myogenic domains gain access to neuronal‑gene promoters, driving lineage drift and ectopic H3K27ac acquisition[1].
• Concurrent chromatin de‑compaction exposes endogenous retrotransposons, allowing their transcription; the resulting nucleic‑acid sensors amplify IFN‑stimulated and NFκB signaling[1].
• Sex difference: higher circulating estradiol in females stimulates NAMPT expression, boosting NAD+ synthesis and partially rescuing cohesin function, thereby limiting TE activation (9 vs 47 TEs in geriatric males)[1].

Testable Predictions

1. Geriatric male MuSCs will show lower nuclear NAD+ and reduced cohesin (RAD21/SMC3) chromatin occupancy than age‑matched females; female MuSCs will exhibit higher NAMPT and SIRT1 activity[1][2].
2. Pharmacological NAD+ augmentation (e.g., NR or NMN) in aged male MuSCs will restore TAD insulation (measured by Hi‑C insulation score) and suppress ectopic neuronal gene expression (e.g., Tubb3, Snap25)[1].
3. Conditional knockdown of NAMPT in female MuSCs will phenocopy the male‑specific increase in TE expression and TAD boundary loss[1].
4. Overexpression of a cohesin‑loading factor (e.g., NIPBL) in aged MuSCs will rescue TAD boundaries without altering NAD+ levels, indicating that cohesin loss is sufficient for enhancer rewiring[3].
5. Simultaneous inhibition of IFN signaling will reduce inflammation but will not restore TAD insulation, placing inflammation downstream of architectural collapse[1].

Potential Experiments

• Perform ATAC‑seq and Hi‑C on FACS‑sorted young, old, and geriatric MuSCs from both sexes; correlate NAD+ levels (mass spectrometry) with insulation scores[1][2].
• Treat cultured geriatric MuSCs with NR (1 g/kg diet equivalent) for 2 weeks; assess neuronal gene markers by qPCR and TE expression by RNA‑seq[1].
• Use degron‑mediated acute depletion of NAMPT in female MuSCs; monitor TE activation and H3K27ac at neuronal enhancers via ChIP‑seq[1].
• Rescue experiments: overexpress NIPBL via lentiviral vector in NR‑treated male MuSCs; evaluate whether TAD recovery is additive or epistatic[3].
• In vivo: administer NMN to aged male mice for 3 months; isolate MuSCs and perform single‑cell multi‑omics to track lineage fidelity and inflammation[1][2].

If NAD+‑cohesin axis proves causal, restoring NAD+ or bolstering cohesin loading should reverse enhancer rewiring, curb lineage drift, and mitigate inflammaging in a sex‑specific manner. Failure to rescue TAD insulation despite NAD+ supplementation would falsify the hypothesis and point to alternative drivers of 3D genome collapse.